Treason
by Eplen91
Summary: When the SGC sent a request for him, he didn't know what to expect but he didn't in a million years expect to be arrested by the FBI.
1. You have the right to remain silent

**Title:**** Treason**

**Author:**** Eplen91**

**STARGATE: ATLATIS**

**Rating:**** T for content and language**

**Spoilers:**** There is some referring to The Return, Miller's Crossing and Outcast**

**Genre****:**** Drama/Crime**

**Setting/Season: **_**Season 5 **_

**Summary:**** When the SGC sent a request for him, he didn't know what to expect but he didn't in a million year expect to be arrested by the FBI. **

**A/N: Not much to say, just that I want to thank my Beta, Drey'auc475, for the amazing job. There something wrong with this site. So I had to upload it again. Sorry for that.**

**Disclaimer: ****I don't own anything. I wish I did. :D **

Chapter 1: You have the right to remain silent

The mess hall was always crowded at this time of the day with people who were eating, playing some sorts of games or just relaxing. Amongst people that were playing games sat Colonel Sheppard and Rodney who were playing chess.

"You cheated!" Rodney exclaimed.

"No I didn't. How can someone cheat in chess, McKay?" Sheppard replied.

Rodney thought for a moment, "You have a good point there. But still – how can someone start losing so many Chess pieces and then get check."

Sheppard was about to make a move with his king when his earpiece buzzed. He tapped his ear piece. "This is Sheppard."

"_Colonel,_" came the base leader, Mr. Woolsey's voice._ "Can I see you in my office?"_

"Yeah, I'll be there in a minute." He stood up. "I'm sorry, Rodney, but Woolsey wants to see me. We'll have to finish this some other time."

_Wonder what Woolsey wants_, Sheppard thought as he walked out of the mess hall.

"You wanted to see me, Sir," the colonel said as he entered Woolsey's office.

"Have a seat, Colonel," Woolsey offered, gesturing towards the chair.

Sheppard sat down. "So," he said cautiously. "What is it you wanted to talk about?"

"Stargate Command has sent a message. They are requesting your presence."

Sheppard frowned, immediately suspicious. "Did they say why?"

"No. They didn't." Mr. Woolsey looked at Sheppard. "I'm sure it's important. I doubt they would send a request for you if it wasn't."

"But, don't you think that it's a little strange that they haven't told you why they want me back on Earth."

"Yes, but I don't think we have choice. It was actually General Landry's orders." Mr. Woolsey leaned his elbow on the desk. "You leave in an hour."

Sheppard blinked with surprise and stood up to get himself ready in a slight daze.

------

Sheppard was in his room, packing his bag, thinking about why the SGC had sent a request for him without telling why. He was about to close his bag when the door slide open.

"I heard that you are going back to Earth," Rodney said,

"Yes, I am, Rodney," Sheppard replied, without looking up from his packing.

"Do you know why they sent a request for you?"

"No, I got no idea." He wondered if it had something to do with his brother, Dave, but they would have told him if that were the case.

There was an awkward pause before Rodney coughed "I better go. Jennifer is probably waiting for me. Have a nice time on Earth." Rodney turned and left the room. After the astrophysicist had left the room, Sheppard grabbed his bag and tossed it over his shoulder, leaving his room and heading for the Gate Room.

-----

When Sheppard arrived at the Gate Room, Mr. Woolsey was waiting for him. Sheppard went over to Woolsey and put his bag on the floor. "Are you seeing me off?"

"Yes. I just wanted to wish you good luck." Woolsey extended a hand.

"Thanks, Mr. Woolsey," Sheppard replied, shaking his hand. Mr. Woolsey gave a signal to Chuck to start dialing the gate. As John stood watching the 'gate spin, a strange feeling he was in some sort of trouble washed over him. But there was nothing outstanding that he could be held accountable for, so he just shrugged it off and stepped through the 'gate.

Stepping on the other side to Earth he saw couple of soldiers waiting for him at the base of the ramp.

He moved his gaze up and saw General Landry watching from the Control Room. Seeing the look on the general's his face made Sheppard's stomach turn. Something was wrong. One of the soldiers stepped closer to the ramp, meeting Sheppard. "Colonel Sheppard. Can you please follow us?"

Sheppard hesitated a little but walked down the ramp and let himself be led out. Noticing that people walked past them were stopping to watch made him feel he was being escorted to his execution. His heart began to pound a little harder.

"Can you tell me where we're going?" Sheppard asked, looking at the soldiers beside him.

"I'm sorry," the taller of his escorts said, "but I can't discuss it with you. I have orders from General Landry not to."

John made a show of looking around them. "Well, I don't see Landry here, so you can tell me. He doesn't need to know."

"I'm sorry, Colonel, but I'm not going to disobey orders from the General." The soldier stated and continued walking.

It wasn't long before the colonel realized they were heading for the surface. Stepping from one elevator to the next he leant against the back wall of the elevator nervously. What the hell was going on? Where were they taking him? Why was he suddenly on a need to know basis?

Once they were out in the car park, Sheppard spotted couple of black SUVs and copper-types standing behind the military gate. The soldiers escorted Sheppard out the gate and walked back into the security checkpoint. Some of the suited men quickly rushed over to Sheppard and handcuffed him. He tried to resist but there was no point. They had him in a tight grip.

"What is going on?" Sheppard asked confused. He had dropped his bag in the slight scuffle and a suit-clad wall of muscle picked it up and carried it over to one of the SUVs.

One of the suits stepped in front of Sheppard and flashed a badge at him. "Lieutenant Colonel John Sheppard, I'm Special Agent Connor from FBI. You are under arrest for treason and espionage against the United State of America, and for the murder of the Russian ambassador Sergei Petrov and his wife, Elena Petrova," he told him, stepping closer. "You have the right to remain silent…"

Everything began to spin and Sheppard couldn't hear the agent anymore; he only saw a mouth moving. He had problem wrapping his head around what was happening to him. He had a feeling something was wrong from the minute Woolsey had told him Stargate Command had requested him back on Earth, but not in a million years would he have thought he would be arrested for treason and espionage, let alone murder.

"…If you cannot afford an attorney, one will be appointed to you. Do you understand these rights as they have been read to you?" The agent finished speaking, glaring wickedly at the colonel with a satisfied smiled around his mouth.

Sheppard nodded slowly and he was escorted into a black SUV.


	2. I’m telling you, that isn’t me

**I'm back! Thanks for the reviews! Well… there is not much to say so on to the story. **

Chapter 2: I'm telling you, that isn't me

Sheppard was lying on a bed in a cell that was barely six feet wide, thinking about what had happened. He had still problems wrapping his head around what had happened. He was innocent, but looking down at the orange prison jumpsuit made him feel like a criminal. He heard footsteps that stopped outside his prison cell and then he heard a rattling keychain. He lifted his head a little, looking at the prison cell door. The door opened and an escort of two agents came in.

"Stand up," one of the agents ordered. He stood up, heart in throat, and was escorted out of his cell.

-----

He was taken to a room that contained a table and two chairs, one of which was occupied by a female agent perusing a file. She looked up at him as he entered.

"Colonel Sheppard. Have a seat," the woman greeted, gesturing towards the spare chair. Rough hands shoved Sheppard down on the chair. "I'm Special Agent Moore," the woman continued. "I'm the agent who is going to lead this investigation." She paused. "I'm sure that Agent Conner read your rights but I'm going to read your rights again before we start this interrogation so you understand." The agent gave him a satisfied smile. "You have the right to remain silent and refuse to answer questions. Do you understand?

Sheppard considered telling her where to stick it. But he knew that wouldn't get this mess sorted. So he answered, "Yes."

"Anything you do say may be used against you in a court of law. Do you understand?"

Why were they treating him like an idiot? "Yes."

"You have the right to consult an attorney before speaking to us and to have an attorney present during questioning now or in the future. Do you understand?"

It was bad enough they thought he was a criminal. "Yes."

"If you cannot afford an attorney, one will be appointed for you before any questioning if you wish. Do you understand?"

Perhaps it was just protocol. "Yes."

"If you decide to answer questions now without an attorney present you will still have the right to stop answering at any time until you talk to an attorney. Do you understand?"

Well, whatever it was, she was starting to get on his nerves. "Yes."

"Knowing and understanding your rights as I have explained them to you, are you willing to answer my questions without an attorney present?"

Did he have any choice in the matter? He didn't suppose there was a lawyer on the planet that would believe him if he told them the truth. "Yes."

"Sign here." Agent Moore handed him a piece of paper to sign. Sheppard sighed and took the pen she held out, signed it and handed it back.

"Let's get started," Agent Moore smiled and folded her hands. "How long have you been working for the Russian mafia?"

His eyes widened. What the hell? The Russian Mafia? "I haven't been working for the Russian mafia."

"Colonel, we have proof," she said, "that you have been trading information about the US government and the US military in the exchange for jewels, and that you have been hired as a hit man for the mafia to eliminate the Russian ambassador, Sergei Petrov. Apparently they weren't happy with the work Mr. Petrov did. And unfortunately Mrs. Pretova got in the way; but that didn't stop you." She took out a digital recorder out of her pocket and put it on the table and pressed play.

"_Colonel, I have a job for you." _

Sheppard could clearly hear that the man on the tape was from Russia because of the heavy accent. The voice was a deep baritone that distorted slightly as it came from the tiny speaker.

"_What kind of job? You owe me for the information I gave you about the government and the military information."_

Sheppard felt his eyes widen at the voice that was so clearly his own. This wasn't possible!

"_Relax__, Sheppard, you'll get your jewels. But first, I have a job for you." _

"_What kind of job?" _

"_Remember Sergei Petrov? We aren't quite happy with his work and we want him eliminated. __You have 48 hours to get rid of him and I want proof that he is dead. After that you'll get your reward." _

Agent Moore pressed the stop button, and looked at Sheppard like he was already convicted. He supposed in their eyes he was.

"That isn't me!" he almost cried, trying to convince the agent that he was innocent. "It sounds like me but that isn't me, I'm telling you."

Moore put the recorder back in her pocket and took out some pictures and put them in front of the colonel so he could see. Sheppard looked at them, each glossy 6x4 leaving him more confused than the last. They were pictures of him getting out of a car, sitting on a park bench talking to a strange man, pictures of him sitting in a restaurant talking to the same man that was on the picture of him on the park bench and pictures of him handing over a suitcase. The date stamp on the bottom of the pictures said they were from two weeks ago. How could that be? He'd been in the Pegasus Galaxy for the last four months. "That isn't me," he said again, sounding like a broken record even to himself.

"Colonel, this is just some of the pictures of you," she said, "and do you really think I have an IQ of 40?" she asked and picked up one of the pictures, showing it to one of the agents, who were standing near the door. "Tell me, Agent O'Brien. Is it my imagination or is this a picture of the colonel?"

Agent O'Brien nodded. "Yes, Ma'am, that is a picture of the colonel."

She turned back to Sheppard and put the picture on the table. "I rest my case."

"I'm telling you, that isn't me."

Moore ignored him and showed him another picture of him talking to a woman. He looked closer at the picture. It was a picture of him at his father funeral, talking to Ava Dixon. The photo looked like it had been taken through a window but clearly showed his profile as he spoke with Ava. How the hell had they gotten _that _photo? And why did they have him under surveillance _then_? He baulked but tried not to show it.

"Can you tell me who this woman is?" she asked.

"I don't know her," he lied.

She leaned her elbows on the table and leaned closer to Sheppard, smiling falsely. "I have been up since o-six-hundred this morning and I've been working twelve hours without a break – my patience is wearing very thin with you. So I advise you to answer my questions." She leaned back in the chair.

"How the hell can I answer your questions when I don't know the answers? I'm innocent!" His voice was rising as his own patience was waning. There was only so many times he could say that they had the wrong guy.

Moore leant forward again and stabbed the photo with a finger. "Again, who is this woman?"

"I don't know."

"Let me tell you something, Colonel, I have friends in the Pentagon, so if you give me some names, I'll put in a good word for you. We only want names and I can assure you that the Air Force Office of Special Investigations won't give you an opportunity like this when they get their hands on you."

"For the last time," Sheppard said trying to control his temper. "I'm innocent. I haven't been working for any mafia, and that man in those pictures isn't me." He slammed his fist on the table. Within a heartbeat Sheppard was surrounded by several agents and staring at the barrels of their handguns.

"Take him back to his cell." Agent Moore ordered with a dismissive wave of her hand.

Two agents grabbed a hold of the colonel and escorted him out the integration room and to his prison cell.


	3. You get twentyfour hours to come clean

**Thanks for the reviews! And once again I want to say thanks to my beta, Drey'auc475. I also want to add that ****G-****Man**** is short for Government Man and its slang for a FBI agent.**

Chapter 3: You get twenty-four hours to come clean

Mr. Woolsey sat in his office; reading over the message he had received from the SGC. He had so many thoughts when reading it over. At that moment someone knocked on his door. Looking up and saw Teyla, Rodney and Ronon standing in the doorway.

"You wanted to see us?" Teyla asked, stepping into the commander's office with Ronon and Rodney behind.

Woolsey set aside the message and sighed. "Yes, it's about Colonel Sheppard," he said. "You all know the colonel was requested back to Earth, and –".

"Is Sheppard hurt?" Rodney asked worried, cutting Woolsey off. He already didn't like the way this conversation was turning. Rodney looked over at his other teammates. He could tell that Teyla and Ronon were becoming worried for their team leader as well.

"We don't know –". He was cut of again but this time by Ronon.

"What do you mean about 'we don't know'?" Ronon asked, almost demanding an answer.

Woolsey sighed. "Yes, we don't know because Colonel Sheppard has been arrested by the FBI for treason, espionage and murder. But I highly doubt that the FBI would hurt him."

Rodney, Teyla and Ronon looked at each other. They all were in shock. Ronon crossed his arms. "FBI?"

"The FBI is an agency of the US government that serves as both a federal criminal investigative body and an internal intelligence agency. The FBI has investigative jurisdiction over violations of more than 200 categories of federal crime." Mr. Woolsey explained.

Ronon frowned. "What?"

Rodney sighed and said, "To dumb it down for you Conan, they put you in jail if you commit a crime that threatens the country, government or lots and lots of people."

Woolsey nodded apologetically to the Satedan. "Right. I'm going back to earth to assist the colonel. I've asked Major Lorne to keep Colonel Sheppard's chair warm. Rodney, you're in charge until we get back."

"Me?" Rodney asked, surprised.

"Yes. You're a senior member of this expedition, so with Colonel Sheppard and me on Earth, you are in charge." Woolsey said. "I'm leaving in an hour."

**_----_**

Woolsey looked at the gate spin. He was anxious to get to earth and help Sheppard. He had come to think of the colonel as his best ally on this base. Without him it was clear the military contingent in the city would fail. As Mr. Woolsey was waiting in the gate room, major Lorne approached him. "Major Lorne," Mr. Woolsey greeted. "What can I do for you?"

"I wanted to wish you good luck," Lorne said. "And ask if you tell Colonel Sheppard everybody here wants him back home and safe."

Woolsey smiled. "I can assure you major, that I'm going I can to get Colonel Sheppard back," he assured the major.

He nodded in understanding. "I better get back to work." Major Lorne excused himself and headed out of the gate room. Mr. Woolsey turned back to the Stargate and sighed. When the gate had established a wormhole to Earth, Mr. Woolsey stepped through the 'gate with a sense that getting Sheppard out of the custody of the FBI wasn't going to be easy.

On the other side of the wormhole he was met by General Landry. Woolsey walked down the ramp to the general with an extended hand. "It is always a pleasure to see you general, but I wish it was under different circumstance."

"Likewise, Mr. Woolsey," General Landry replied, shaking the Atlantis commander's hand. Woolsey followed Landry up to the briefing room, where General O'Neill sat, waiting for them.

O'Neill stood up as they entered the briefing room. "Long time no seen." O'Neill extended hand.

"Yes, it has," Mr. Woolsey replied, shaking O'Neill's hand. He was actually surprised to be greeted so warmly by both generals. Before taking his post on Atlantis, the IOA operative had caused his fair share of headaches for both men before him.

"Shall we begin?" General Landry sat down.

"Yes; that's a good idea," Woolsey said as he sat down next to O'Neill.

"I've spoken to the president," General Landry began, "and he said that he has seen the evidence the FBI have. The evidence is from the time when the expedition were back on Earth because of the Ancients. There's also additional footage from when Doctor McKay, Dex and Sheppard were on Earth because McKay's sister; and when Sheppard was at his father's funeral." He paused, folding his hands on the table in front of him. "The murder of the Russian ambassador took place while Colonel Sheppard was at his father's funeral. A week after the murder the FBI got pictures of Sheppard and a tape recorder by an anonymous person who apparently works for the Russian Mafia. And now they've turned up some other pictures of the colonel. The president said he hasn't any choice but to believe these allegations, and if Colonel Sheppard is working for the Russian mafia, he would have someone working with him. "

"Is there any chance the mimic devices from Area 51 have been stolen again?" General O'Neill asked, the memory of when he was charged with the attempted murder of Senator Kinsley fresh in mind.

"No; they've gone over the facility twice," Landry told him. "And the fact the director of FBI reports to the Director of National Intelligence, who in turn reports to the President and both of them are good friends, doesn't help us very much."

"Ah great," General O'Neill said sarcastically. "Even if Sheppard isn't on Earth, he managed to get in trouble here. That's amazing."

"Do you know where Sheppard is being held?" Woolsey asked.

"Yes. He is being held at The United States Penitentiary in Florence."

"Well, its time for me to see Colonel Sheppard." Woolsey said. "Gentlemen," Mr. Woolsey excused himself, gathered his things and headed for the door.

**_----_**

Sheppard was holding his tray, scouting at the inmates eating the dinner, looking for a place to sit. He hadn't felt hungry before they mentioned dinner. And for good reason. The food on his tray looked like slop. He wrinkled his nose and grimaced.

He noticed one of the inmates was getting ready to leave from the table, and Sheppard got ready to take the place. Taking a step forward, he heard someone whistle at him. He stopped and looked over his shoulder, where the whistle sound came from. Five very large, muscled and tattooed men sat at a table in the nearest corner of the cafeteria. One of them signalised to him to come over.

_Suck it up Sheppard, you have fought creatures that can suck the life of you with their hands. _he said to himself mentally,_ five inmates won't be a problem for you,_. When he arrived at the table, one of the men reached out a hand. "I'm Big B."

Sheppard stood stunned for a moment, staring at the offered hand. His senses suddenly went into overload wondering what their angle was. Big B laughed and said, "What's wrong, dog? Ain't gonna bite you."

Setting his tray on the table Sheppard cautiously shook his hand. "I'm John." Well, weren't these the nicest criminals in the cell block. Either that or perhaps Sheppard had seen too many prison movies.

"How's it hangin', dog. That's Cruiser, Black Jack, X-Ray and Kid Ice," Big B gestured at them in turn, as Sheppard took a seat at the table. "So, John, what are you in for?"

The colonel couldn't help the bitter grin on his lips. "Treason, espionage and murder."

"That's some crazy shit, man," Big B said. "You know, we had a fish which was put here with the same charges as you. Real wimp he was. After his integration, he told Kid Ice here the G-man who was interrogatin' him had these glowin' eyes."

Sheppard choked on his water. "What did you say?" he asked, wiping his chin on his tacky orange jumpsuit.

"Glowin' eyes was what he told," Kid Ice said. "Fool was crazy."

_Holy shit_, Sheppard thought. "What happened to him?"

"He got transferred to ADX Florence but he never made it there."

"He didn't?" Sheppard asked, a frown forming on his brow.

Big B shook his head. "His transport was attacked, and there's dis rumor going on he was found without a head."

Sheppard opened his mouth to respond but was cut off by three prison guards walking toward him.

"Stand up, Sheppard," one of the prison guards ordered. "You're coming with us." The guards grabbed a hold of Sheppard by his shoulders and escorted him out.

"Bye, Sheppard," he heard Big B call. "We'll save a seat for you at dinner!"

Sheppard was taken to the integration room again. A face Sheppard hoped not see again smiled at him. "I'm so sorry to have disturbed you, Colonel." The guards shoved Sheppard down into the chair.

"You are probably wondering why you have been brought back," Agent Moore smiled.

"Not so much actually," Sheppard replied as casually as possible.

"Well, I decided to give you a second chance to come clean."

"Really? Is that so?"

"Yes. When you understand what kind of prison sentences you can get, then I think you'll change your mind about my earlier offer." She paused, smiling. "You see Colonel, it is your ass that's on the line here, not mine." She paused again. "Going by the book we'll charge you with murder of a foreign official. Sentence: death penalty or imprisonment for life. Then we'll charge you with gathering and delivering defence information to aid foreign governments. Sentence: death penalty or imprisonment for thirty years. And last but not least, treason. Again, the sentence for that is the death penalty or life." After completing her monologue of the various reasons Sheppard why would die by execution, she folded her hands. "You get twenty-four hours to come clean."

"Nice to know," he said bitterly.

"Colonel, I have no sympathy for you," she said coldly. "If I had authority to send you to Guantanamo Bay, you would have been on the first flight to Cuba."

"You know I've always wanted to live some place tropical."

The woman sneered at him. "I'm finished with him." Agent Moore told the prison guards. The guards grabbed Sheppard, hauled him out of the chair and frog-marched him to the door. "One other thing, Colonel," Agent Moore said with a melodic, and creepily calm voice. The guards stopped and turned Sheppard so he was facing the agent. Sheppard felt a chill travel down his spine and he could feel the hairs on the back of his neck rising. "Ask yourself a question," she said. "Would you rather serve your sentence in a military prison or in a federal prison? Because as I said, I have friends in high places and they can arrange so that you get a dishonorable discharge and serve your sentence in a federal prison. And you'll only get 25 years. If you don't want to make a deal, rest assure Colonel, a court-martial death sentence will be hanging over you." Sheppard could see the satisfaction in her smile. "To bad Alcatraz is closed. Right, Colonel?" Agent Moore smirked cruelly at him.

"Right," Sheppard managed to mutter before he was dragged out of the interrogation room by the guards. _And I thought things couldn't get any worse._


	4. Dead man walking

**I am back with chapter 4. Sorry that it have taking me so long to update. I have been sick and I have been busy with school and applying to universities. But here is chapter 4. Enjoy! =D**

Chapter 4 – Dead man walking

John's head was pounding. His lip was swollen where a fist had busted the skin, a black eye was beginning to form, his nose was bruised and his ribs were sore. Somehow he had forgotten rule Number One of 'how to survive in jail': _don't stare another inmate._ He had been out in the prison yard with the other inmates, when he had realised too late he had been staring.

Upon hearing,_ "What are you looking at, pretty boy?"_ he knew he was in trouble. If it hadn't been for his prison 'buddies'_,_ he would probably be laying in the morgue right now. The only thing that had gone his was today was that he had been moved to another prison cell that was a little bigger and in the main complex; although he wasn't sure this was a good thing. Sheppard had gotten through most of his first day in prison. The only thing he wasn't looking forward to was showering. He knew that when you dropped the sop on the floor, whatever you do never pick it up.

Hearing footsteps further down the hallway he sat up in his cell and sighed. The footsteps became louder and louder and when they stopped, he saw two prison guards outside his cell.

"Stand up, Sheppard. Somebody wants to see you," the shorter of the guards told him.

"Lemme guess, Agent Moore has more questions," Sheppard replied casually as he stood up.

The cell door opened and the guards entered. They put a hand on Sheppard's shoulder and guided him out of his cell.

"No, your lawyer wants to see you," The other one said as Sheppard was marched toward the interrogation room.

_**XX **_

When Sheppard entered the interrogation room (which he was becoming quite familiar with) he saw Mr. Woolsey. His heart skipped a beat or two in happiness. He had never been so happy to see Woolsey. He was shoved down on the chair. To Sheppard's surprise the guards left the room leaving only Woolsey and John in the room. The commander noticed the surprise look on Sheppard's face.

"The prison director is an old friend of mine," Woolsey said. "He owes me a favor. But how are you? And what have happened to you?" Mr. Woolsey asked, referring to Sheppard's black eye, swollen lips and to his bruised nose.

"Long story," Sheppard told him. "Tell that you are here to get me out." Sheppard leaned closer to Woolsey. "They think that I killed a Russian ambassador and his wife, and that I've given information about the military and the government. That's crazy because I've been on Atlantis."

"I know, Colonel, but they have presented evidence to the President and he had no choice but to believe these allegations. And we have to be careful so the FBI doesn't get to know about the Stargate program. But we are doing everything we can't do for you."

"Are Teyla, Ronon and Rodney at the SGC?" John asked, realizing that he was missing his friends.

"No they are in Atlantis still. Colonel, is there anything I can get you?" Woolsey asked, looking at the colonel, who was looking tired and bruised. The IOA representative studied John's face. A kind of sadness had fallen over the colonel, reflected in the puckering of his eyebrows. Deep inside, he knew Sheppard was freaking out. With these allegations and prison sentence that John was facing, any man would have been scared. Woolsey felt a great deal of sympathy for John. He really wanted to get the poor man out.

"Well, a turkey sandwich would be nice," Sheppard managed to smile a little.

Mr. Woolsey smiled. "That I think I can manage."

At that moment the door slammed opened and in came several agents in lead by the agent Sheppard recognized from when he had been taken in custody by the feds, Agent Connor. Two of the agents took a hold of Sheppard, dragged him up from the chair and marched out from the room. Mr. Woolsey stood up in a hurry. "What is the meaning with this?" Woolsey asked, demanding an answer from the agent.

"We've gotten some threats from Russians and we've decided to move Colonel Sheppard to Administrative Maximum Facility," Connor explained to Woolsey. "You can visit your client there." Connor walked out leaving Mr. Woolsey startled.

_**XX**_

Sheppard had been pacing back and forth in his tiny cell. His brain was in high speed now. He was more stressed than he'd ever been before. He concluded that must be dreaming because this wasn't happening to him. He stopped as the prison door opened and in came four agents. One of the agents keeled and put on leg irons. He stood up and handcuffed him, and then they escorted Sheppard out of his cell. As they walked, inmates walked up their prison doors and began to shout.

"DEAD MAN WALKING!" one the inmates shouted as they walked past his cell. Apparently the other inmates thought it was funny and started to shout 'dead man walking'. John didn't feel comfortable at all but continued to walk with his head held high showing that it didn't bother him at all.

Walking out side Sheppard spotted his transport. They opened the door and almost pushed him inside. Sheppard sat down, leaned his head backwards, closed his eyes and prayed that when he opens his eyes again he would be back at Atlantis. After ten minutes sitting still, John felt the vehicle move.

Twenty minutes passed and John's thoughts went to the man who had been found in the woods with out a head. The vehicle came to a stop and Sheppard felt his heart began to beat slightly faster. John was about stand to ask what was going on but before managed to do so he heard gunfire. He rapidly stood up to reach for the door but he didn't come so far before the door opened and somebody threw something in and in moments the back of the transport was filled with gas, and then everything went competently black.

_**XX**_

Sheppard's eyes slowly fluttered open. His head felt like he had been smashed into a brick wall. His legs and hands were tidied to a chair. He looked around. He was in an abandoned warehouse. His eyes fell on a table covered in various implements ranging from butcher's knives to hand held tools, and a huge man walking towards his with an evil grin on his face.

"I see that you have woken," The man said. Sheppard could easily hear that the man was from Russia. "How do you feel, Colonel?"

"I'm feeling peachy," Sheppard said dryly.

"Let's get down to business," the Russian said. "Tell me about Atlantis."

"I don't know what you're taking about," Sheppard lied, trying to keep his cool.

"Do not lie to me, Colonel."

"I'm _not_ lying."

The Russian walked over the small table and ran his fingers a pair of pliers where they sat on the table. "You see, Colonel, I don't like when people are lying to me." Leaving the pliers, he said walking closer to Sheppard. Sheppard eyes were almost glued on the pliers on the table, fearing what the Russian was going to do with them.

"I don't know what you're on about. The only Atlantis I've heard of is a Disney movie."

"This is not a negotiation. Each time you refuse we'll take something away from you."

"I don't know!" John yelled. It had been the longest day in his life and he was surprise he had the strength to yell at all.

"Colonel, Colonel," the Russian said looking back a minute before he shot his fist straight into Sheppard's face and then his other into John's stomach. Sheppard lost his breath for a moment and pain filled through his body and all he wanted to do was to curl up in a ball.

"I said," he managed to hiss through his clenched teeth. "I don't know what you're taking about."

The Russian walked over to the table, grabbed the pliers from the table and grabbed a hold of Sheppard shoulder, "Wrong answer, Colonel," the Russian said, pushing the chair backwards and went straight for the Colonel's mouth. The only person to hear Sheppard's screams of pain was the Russian wielding the pliers.

* * *

**The last scene I have gotten a little inspiration from a CSI Miami episode and feedback is always appreciated.**


	5. He’s apparently sleeping with the fishes

Aloha people! I'm really sorry that it has been awhile since I updated but I'm really really really busy. I'm sorry! =D

Chapter 5 - Great, so he's apparently sleeping with the fishes

Mr. Woolsey practically stormed into the briefing room where General Landry and General O'Neill were sitting talking. Woolsey was so furious that he couldn't think straight. How dare the feds send Sheppard to a Maximum Security Facility? He wasn't a criminal. He was a man who was risking his life for his country and for this planet, and now he was charged with treason and espionage against the country he risked was life for. If he could, Woolsey would tell the FBI to put the charges somewhere where the sun doesn't shine.

Realizing Woolsey had entered the briefing room, the base commander stood. Looking at the general Woolsey knew something was wrong.

"I think we have a much more serious problem than we realized," General Landry told the Atlantis commander.

"What do you mean?" Woolsey replied, stepping closer to the chair next General O'Neill.

"We got a phone call from the FBI," Landry said, "Colonel Sheppard's transport was attacked."

"Attacked?" Mr. Woolsey echoed as he sat down next to O'Neill.

"Yes." Landry reclaimed his seat. He was so fed up with the whole ordeal. He wanted his Head of Military back and fast.

"I don't believe in coincidences," O'Neill said, speaking for the first time. "Does the FBI have any suspects or any clue on who may be behind the attack?"

"No but they suspect it may be the Russians, likely trying to get Sheppard out before he tells them anything," Landry replied. "But we know he doesn't know anything."

"How could the Russians know that the feds where moving Sheppard? Unless…" Jack paused, looking at Mr. Woolsey and then at General Landry. "Unless the Russians were tipped off by someone inside the FBI."

"What are you saying? The FBI have mole?" Woolsey asked.

"Well, it won't be the first time," Landry commented.

"I think its time to get Ronon, Teyla and Rodney here so they can help us get Sheppard back," Woolsey stated.

"That has already been taken care of," Landry replied. "They are arriving in three hours."

XX

Mr. Woolsey stood in the Gate Room ready to welcome the remainder of Sheppard's team when they arrived. Woolsey looked at the 'gate, tapping his foot anxiously. Teyla, Rodney and Ronon weren't going to like it when Woolsey informed them that Sheppard was missing and that his transport had been attacked. He was most nervous about how Ronon would react. He wasn't scared of Ronon. He knew that Ronon wouldn't do anything, but still. Woolsey continued to hold his gaze at the Stargate and sighed.

"Incoming wormhole," Walter announced.

The 'gate began to spin and when it had established a wormhole to Earth, Rodney, Ronon and Teyla walked down the ramp to meet Mr. Woolsey.

"Nice to see you all," Woolsey greeted them.

"It is nice to see you too, Mr. Woolsey," Teyla said.

"How are things on Atlantis?" Mr. Woolsey asked looking at them. Rodney opened his mouth to answer but Teyla beat him to it.

"Everything is fine in Atlantis. Everybody is happy with Rodney's leadership," Teyla stated.

"Yeah right," Ronon said sarcastically. "So why are we here? Something happened to Sheppard?" Ronon asked with serious look on his face. He knew something was wrong. He could see it in Woolsey's eyes.

Woolsey looked over at Rodney suspiciously but let it slide. He couldn't wait to return to Atlantis. He turned his gaze at Ronon. "Let's go up to the briefing room. Both Generals O'Neill and Landry are waiting for us." Teyla, Ronon and Rodney followed Woolsey up to the briefing room. As they entered the briefing room both of the generals stood.

"Nice to see you all, I wish it were under different –" Landry managed to say before he was cut of by Ronon.

"Where is Sheppard? What happened to Sheppard?" Ronon demanded to know.

Landry and O'Neill exchanged looks before Landry turned his back at Ronon. "The FBI decided to move Sheppard to a Maximum Facility and on the way his transport was attacked by, we think, the Russian Mafia," Landry explained.

Rodney crossed his arms. "Great, so he's apparently sleeping with the fishes."

"Let's not go there. I don't think the Russians would go to so much trouble just to kill him. So I think he's alive," Woolsey said looking around. "Well, until now that is."

XX

Sheppard was resting his eyes, but he opened them from time to time. The Russian had left him alone in the abandoned warehouse after almost an hour of torture. He was missing two of his teeth, his left eye was so swollen that he couldn't opened it properly and some of his ribs were broken; at least that's what he suspected. He could also feel the blood was dripping from his mouth. The pain was almost unbearable but he had to suck it up and just bite his teeth together. He knew that his friends were going to find him. He had the feeling he wasn't going to wait long for his friends. As the door from the warehouse opened Sheppard eyes rapidly opened and his heart was beginning to beat faster. Sheppard heard several footsteps that were heading towards him.

_Oh God, please, no more_,Sheppard thought as the footsteps became more noticeable. The footsteps came to a halt and to Sheppard's surprise Agent Connor was standing before him. _Thank God, they've found me_, Sheppard thought. But that thought was shattered when Agent Conner sat down on the chair in front of Sheppard, grinning evilly at him.

"How are you feeling, Colonel," Agent Conner said, his eyes passing over Sheppard. "I see that you have met Andrei. He told me you're a hard nut to crack. Why can't you just tell me about Atlantis? Then we'll stop torturing you."

Sheppard didn't say anything; he just glared at the agent.

"Colonel, don't make this difficult; just tell me."

"What does the Russian mafia want with information about this so called 'Atlantis'?" Sheppard asked.

"Have you heard about an organisation named the Trust?" Agent Conner asked, Sheppard pretended to look confused. Connor continued anyway. "We and the Trust are working together. They get you and we get information about Atlantis. I'm not going to tell you everything, so tell me about Atlantis." Agent Connor paused, smiling and continued when Sheppard didn't open his mouth. "Well then," the agent said as he stood up. "Trust me, colonel, if I was you I would have come clean, because the next person you're going to meet is badder than the Devil himself. And, I believe you know each other." Connor smiled cruelly as the door to the warehouse opened again and a figure stepped through.

Sheppard closed his eyes._ 'This can't be happening to me. Wake up wake up, John. You're dreaming.' _Sheppard told to himself repeatedly before opening his eyes again.

It definitely wasn't a dream.

XXX


	6. The FBI's most wanted

**I'm back! I'm really really sorry that it has taken so long! :D Anyway here is chapter 6 and thanks to everyone that have reviewed, added the story to their favourites and those who have added the story to their alert list! I also want to thank my beta drey'auc475 for her amazing job! Enjoy!**

**Chapter 6 – The FBI's most wanted**

Rodney, Teyla, Ronon and O'Neill had been searching the woods beside the road where Sheppard's transport had been attacked for any clues that could shed some light on who had the colonel or where they were holding him. Fatigue was beginning to set in and they knew that for every hour that went by, the chance finding Sheppard alive became slimmer.

"We've been at this for hours," Rodney complained. "Can't we pick this up in the morning," He wanted to find his best friend so bad, but night was beginning to fall, along with the temperature, and his hypochondria was starting to get the better of him.

"Don't you want to find Sheppard?" Ronon growled at Rodney, looking at the scientist over his shoulder with a piecing glare.

Rodney folded his arms and stood his ground. "Of course I want to find him," he said, "but it won't help Sheppard if we all catch pneumonia. Besides, there's nothing here that'll help us unless we find a map that screams 'Sheppard is here!'." Rodney glanced around where he stood and no sooner than those words were out of his mouth, his gaze fell on a shiny metal object that had no place in the forest.

"Hey, check this out," Rodney said and quickly moved to the metal item where it lay on the fallen leaves next to a sizable boulder.

The others stopped searching the ground and joined the scientist.

"Did you find something, Rodney?" Teyla asked while stepping beside him.

"A canister," Rodney replied and kneeled. "Chlorobenzalmalononitrile," he read aloud and looked up at the others. "Tear gas. Who uses tear gas?"

"Oh, there are so many people I can think of who use tear gas," O'Neill replied.

**XX**

Teyla, Rodney, Ronon and O'Neill stepped into the briefing room where Mr. Woolsey was sitting, watching the television. Noticing that Ronon, Rodney, Teyla and O'Neill had stepped into the room Mr. Woolsey turned in his seat.

"Just the people I was thinking of," Mr. Woolsey said. "You made it in time for the press conference."

O'Neill frowned. "Press conference? What press conference?"

"The FBI is holding it now." Mr. Woolsey gestured at the TV.

Rodney, Teyla, Ronon and O'Neill joined him at the briefing table and watched the scene unfolding on the flat-screen.

A room filled with reporters, sitting with notepads, pens, tape-recorders and microphones, showed on the screen. All of them were clearly waiting for someone to step up to the podium. As Special Agent Moore entered the room, followed by Agent Connor, the room was filled with flashes from cameras. The room grew silent as she took her place behind the podium, Connor, a shadow to her left.

"Good evening," Agent Moore began. "Last night, at 9pm, this man, Lieutenant Colonel John Sheppard from the US Air Force –" she gestured to a monitor to her right, where a picture of Sheppard flashed up, and the camera refocused "– managed to escape after the transport taking him to The United States Penitentiary Administrative Maximum Facility in Florence was attacked. Lieutenant Colonel Sheppard has been charged with treason, espionage against the United States of America, and murder of the Russian ambassador, Sergei Petrov and his wife, Elena," Moore paused, shuffled her notes and continued.

"This man is dangerous, trained to kill and a threat to our nation. Individuals with information concerning Lieutenant Colonel Sheppard should take no action themselves, but instead immediately contact the nearest FBI office or local law enforcement agency,"

She paused again to look directly at the camera. "Lieutenant Colonel Sheppard is currently FBI's most wanted person. The FBI is offering a reward of five-hundred thousand dollars for information leading directly to the arrest of Colonel Sheppard. Any questions?"

Instantaneously twenty hands rose into the air, all with questions hoping to be answered.

Moore pointed to a reporter in the front row. "Yes, you?"

"Couple of years ago," the reporter started, holing a tape recorder as far as their arm could reach. "There was another colonel in the Air Force that was charged with the same charges as this Colonel Sheppard. Does the FBI believe that case and this are connected or is it just a coincidence?"

Agent Moore seemed to blanch, and a muscle in her cheek twitched. "No comment," she said. "I think that's enough questions." Agent Moore walked down from the podium, ignoring the reporters' protests, with Connor directly on her heels.

Mr. Woolsey grabbed the remote control and turned the TV off.

"That was, um, interesting," Rodney stated.

**XX**

Sheppard's wrists hurt. Though, admittedly that wasn't the only park of his body that hurt, especially seeing as he'd been tied to a very uncomfortable chair for two days whilst being tortured. Every time the big Russian, Andrei, left the warehouse Sheppard's heart leapt with relief. Not that Sheppard was scared of the oaf, but the Russian was cold. Every time Andrei tortured him, a smirk would come to Andrei's face. Sheppard knew Andrei was a professional. He couldn't wait to get out of here.

Suddenly he heard the door to the warehouse open. He heard footsteps that he was now familiar with; Andrei's footsteps. Arriving in front of Sheppard, Andrei placed the table and chair he carried in front of Sheppard. Then another pair of lighter footsteps could be heard. Moments later, a figure stepped in front of John, giving him a weird sense of déjà vu. He was looking at himself.

"What the –" he blurted as he stared up at the figure.

"Hello, Colonel," his doppelganger said. "Well, isn't this wired?" The other him smirked and placed a hand under his jacket, making the appearance of him to fade and reviled that it was Special Agent Moore, wearing John's image. "Surprised, Colonel?" She smirked and sat down on the chair. Andrei untied Sheppard's left hand, placed it on the table and held it down, so he couldn't move it. Sheppard's heart skipped a beat. Suddenly everything was falling into place.

Moore leaned closer to Sheppard. "Shall we play some Russian roulette, but with a little twist?" She said as her eyes glowed and pulled a very sharp knife from her pocket.

**XX **

Woolsey, Rodney, Teyla, Ronon and O'Neill sat in the briefing room at the Stargate Command, talking amongst themselves when General Landry stepped into the briefing room. All heads immediately turned to the general.

"Is something wrong, General?" Mr. Woolsey asked.

"We think we know where Sheppard is being held," General Landry answered.


	7. Oh my God, what happened to you?

**Hola! I'm really sorry that it has taken so long. Anyways, this is the last chapter in this story. I want to thank my** **awesome beta, drey'auc475, people who have been reading, left a review or two and added the story to their alert list. =D**

**Chapter 7 - Oh my God, what happened to you?**

John was staring at the female FBI agent, who had turned out to be a host for a Goa'uld. He had heard that the Trust had infiltrated different agencies. He remembered the conversation he had back at the prison with the inmates about the other colonel; who had told them about the FBI agent who had been interrogated him had glowing eyes. It made more scenes now and the colonel wasn't as crazy he seemed.

"What does the Trust want with me?" Sheppard asked, glancing nervously at his hand that Andrei was holding down. He looked up at Agent Moore. "And where do you get that mimic device?"

"One question at the time, Colonel. I heard a rumor that your ATA gene is quite strong, stronger than most. But I don't work for the Trust; I work for the Russian mafia. The Trust and Russian mafia is cooperating, and Russians gave this body, how can you put it, as a gift," she said. "After the Trust is done with you, they are going to hand you over to us." She smiled. "You see, Sheppard. We are going to use you to get classified information."

Sheppard let out a laugh. "How are you going to do that, when I'm on the list of FBI's Most Wanted?" Andrei had told him that he was on that list, and that the FBI was offering a reward of five-hundred thousand dollars.

"Well, let's just say the FBI has made a mistake in their investigation."

"And how are you so sure I'm going to cooperate?"

"You have to wait and see, colonel. But let's cut the crap." Moore ran the tip of the knife along one of Sheppard's fingers. "Colonel, tell us about Atlantis."

"As I told your friend here, I don't know anything about Atlantis. Besides if you work with the Trust, how come the Mafia is asking me about this Atlantis?"

"Because the Trust said any information we get out of you, we keep. So cut the bullshit, tell me about Atlantis." Agent Moore demanded.

"I don't know!" Sheppard screamed to the agent's face, hoping that she got the point that he wasn't telling anything.

"Andrei, spread his fingers," Moore order. Andrei did what he was told. Agent Moore lifted the knife, glared at the colonel and placed the knife right between his fingers. Agent Moore smiled. "Next time you only have nine fingers. Tell about me about Doctor Rodney McKay."

"I've no idea who that is."

Agent Moore shoved the chair backwards in anger. "Andrei, turn his chair around," Agent Moore order, grabbed Andrei's gun and pointed the gun at Sheppard thigh. "Last chance, colonel." Sheppard didn't say anything. The agent turned to Andrei. "Андрей, получите коробку," Moore ordered in Russian. After watching the Russian leave, the FBI agent turned and fired a shot into Sheppard's thigh. Sheppard's scream of agony cut through the noise of the gunshot. The pain made him growl through his gritted teeth. It felt like a thousand knives piercing his body, and he felt the vital blood oozing down his leg.

"I'm not a sadist," the FBI agent growled at a Sheppard, "but I surprisingly enjoy watching you suffer. And I'll continue make you suffer if you don't start talking," John glared at her through the pain. He may have a high threshold for pain, but that didn't mean he couldn't feel it.

The door to the warehouse opened, and Agent Moore looked up and smiled. Andrei re-entered the warehouse. She stood up. "Do you have them with you?"

Andrei lifted a box that looked very similar to a cooling box for organs. The hairs on the back of Sheppard's neck were rising with every step Andrei took, and a fear got a hold of him. His eyes were glued on the box until Andrei had placed it on the table in front of him.

"Relax, Sheppard. We aren't going to take your heart," Andrei said, opening the box to revile the contents of the box; Goa'ulds.

"The choice is yours Colonel, which of them do you want?"

Sheppard was about open his mouth to response, but was cut off by noises that came outside the warehouse.

"This is the FBI!" someone shouted from outside of the warehouse. "We have surrounded the building. Surrender!"

Sheppard's heart skipped a couple of beats. Finally, they had found him. Sudden calm filled him at the thought of seeing his friends again; playing chess with Rodney, training with Teyla, drinking beer and watching movies with Ronon. But he had to get out of the warehouse first.

He could see Andrei and the dirty FBI agent were panicking. To Sheppard's shock Moore grabbed the gun off the table and pointed Andrei's own weapon at him. Tears escaped Agent Moore's eyes. "I'm really sorry, Andrei," she whispered, and in front Sheppard's eyes she shot Andrei in the head, immediately killing him. Moore untied Sheppard's other arm, grabbed him and pushed him to the floor. Pain flooded through Sheppard's body as he used his good leg and kicked Moore's feet from under her. Kicking the gun away, Sheppard stood and began a difficult limping run towards the door.

Behind him, Moore retrieved her gun and scrambled to her feet again, taking aim at the limping Sheppard and firing a bullet into Sheppard's shoulder. The colonel went down with a cry of agony.

Smiling, she walked over to Sheppard, who was lying on the floor clutching his bleeding shoulder. "Did you really think that I was going to let you go?" she asked with a laugh in her voice. "Oh no, Colonel, if I'm going to die today I'm taking you with me." She lifted the gun to Sheppard, aiming right between his eyes. Sheppard's temple was covered with sweat as he held his breath, his heart beating faster than ever. Agent Moore tighten her grip around the gun and placed a finger on the trigger, but before she could fire the shot, another shot rang out. The agent fell to the ground beside him, looking at him with empty eyes. She was dead. A second later the warehouse was stormed.

"JOHN!" a very familiar voice yelled, Teyla. Sheppard lay his head down, breathed slowly in relief and closed his eyes, he was going home.

"Oh my God, Sheppard, what happened to you?" The voice belonged to his best friend and his brother from another mother, Rodney McKay. He smirked to himself at the cliché.

Sheppard opened his eyes and looked at his friends a moment before he closed his eyes again.

**XX **

John's eyes opened. He was breathing heavily and the sweat was pouring from his temples. He looked around; he was in the infirmary at the Stargate Command. He breathed a sigh of relief. He'd had one of his nightmares again. He'd been having the same nightmare since they had gotten him out of that warehouse. He took another deep breath and glanced at the body that was slumped into the chair besides his bed, asleep. Rodney hadn't removed himself from that chair since John had woken from the surgery. The scientist had told him everything that had been going on at Atlantis and how everyone was waiting for him to come home. And of course, he had told him how he had been acting as the commander of the Atlantis expedition while Mr. Woolsey had been here on Earth.

A dictator in the making maybe, Sheppard joked to himself, smiling. Rodney's eyes slowly flickered open, and rubbed his face before he shifted his position in the chair. Rodney looked at his best friend, smiling.

"Another nightmare?" Rodney asked.

"Yeah," John replied.

"How are you feeling?"

"Like I've been to Hell and back," Sheppard said, giving Rodney a tight-lipped smile. "But Doctor Lam said that I'll be back in Atlantis in no time. But I have to fix my teeth before I leave. Atlantis can't have military commander with missing teeth." Sheppard looked down at his hands. First he had to recover from his injuries, and after that came the hardest part of his recovery, his mental health. Doctor Lam had told him that in order to get over his traumatizing experience he would have to get counseling. He knew that it was going to take a time before his nightmares were going to stop, but at least he had his team beside him. He looked up at Rodney.

"We are going to help you through this, John," Rodney assured him.

"I know," Sheppard said. "Just like I knew you guys would find me." I'm going home,Sheppard reminded himself as he shifted his gaze at the roof.

The worst of it was all over. He was in one piece (give or take) and he could finally put it all behind him.

"I'm hungry," Rodney whined, and John had never been so happy to hear those words.


End file.
